Chimpanzee genomic diversity reveals ancient admixture with bonobos

TLDR

Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high‑coverage whole genomes of 75 wild‑born chimpanzees and bonobos from 10 African countries. The study shows that chimpanzee population substructure predicts geographic origin, and that gene flow from bonobos into central and eastern chimpanzees occurred 200,000–550,000 years ago, contributing less than 1% to central chimpanzee genomes, indicating widespread admixture during hominid evolution.

Abstract

Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales. Multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another, possibly more recent contact (after 200,000 years ago), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.